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Yorodumi- PDB-3mj9: Crystal structure of JAML in complex with the stimulatory antibod... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3mj9 | |||||||||
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Title | Crystal structure of JAML in complex with the stimulatory antibody HL4E10 | |||||||||
Components |
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Keywords | IMMUNE SYSTEM / IMMUNOGLOBULIN TANDEM DOMAIN / RECEPTOR-ANTIBODY COMPLEX / CELL ADHESION / CELL JUNCTION / GLYCOPROTEIN / IMMUNOGLOBULIN DOMAIN / MEMBRANE / COSTIMULATION / HAMSTER IgG / TRANSMEMBRANE | |||||||||
Function / homology | Function and homology information monocyte extravasation / Cell surface interactions at the vascular wall / gamma-delta T cell activation / neutrophil extravasation / positive regulation of epithelial cell proliferation involved in wound healing / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis ...monocyte extravasation / Cell surface interactions at the vascular wall / gamma-delta T cell activation / neutrophil extravasation / positive regulation of epithelial cell proliferation involved in wound healing / heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / bicellular tight junction / cell adhesion molecule binding / neutrophil chemotaxis / integrin binding / protein homodimerization activity / nucleoplasm / plasma membrane Similarity search - Function | |||||||||
Biological species | Mus musculus (house mouse) CRICETULUS MIGRATORIUS (Armenian hamster) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.95 Å | |||||||||
Authors | Verdino, P. / Wilson, I.A. | |||||||||
Citation | Journal: Structure / Year: 2011 Title: Molecular insights into gamma delta T cell costimulation by an anti-JAML antibody. Authors: Verdino, P. / Witherden, D.A. / Ferguson, M.S. / Corper, A.L. / Schiefner, A. / Havran, W.L. / Wilson, I.A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3mj9.cif.gz | 270.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3mj9.ent.gz | 222.2 KB | Display | PDB format |
PDBx/mmJSON format | 3mj9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mj/3mj9 ftp://data.pdbj.org/pub/pdb/validation_reports/mj/3mj9 | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 30647.387 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN (UNP RESIDUES 21-280) / Mutation: K124R, R211Q Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mus musculus (house mouse) / Gene: Amica1, Gm638, Jaml / Plasmid: PMT/BIP/V5-HIS A / Production host: DROSOPHILA MELANOGASTER (fruit fly) / References: UniProt: Q80UL9 |
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#2: Antibody | Mass: 22784.334 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC Source: (natural) CRICETULUS MIGRATORIUS (Armenian hamster) / Strain: HYBRIDOMA |
#3: Antibody | Mass: 23653.455 Da / Num. of mol.: 1 / Source method: isolated from a natural source Details: HL4E10-SECRETING HYBRIDOMA WAS PRODUCED BY FUSING MOUSE MYELOMA CELLS WITH SPLEEN CELLS FROM AN ARMENIAN HAMSTER IMMUNIZED WITH 7-17 DETC Source: (natural) CRICETULUS MIGRATORIUS (Armenian hamster) / Strain: HYBRIDOMA |
#4: Polysaccharide | alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Sugar |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.73 Å3/Da / Density % sol: 55 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 1.2-1.4 M NA-MALONATE, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-D / Wavelength: 0.9793 |
Detector | Type: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 22, 2006 Details: SI(111) DOUBLE CRYSTAL MONOCHROMATOR. ADJUSTABLE FOCUSING MIRRORS IN K-B GEOMETRY |
Radiation | Monochromator: DOUBLE CRYSTAL CRYO-COOLED SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→30 Å / Num. obs: 18365 / % possible obs: 97.7 % / Observed criterion σ(I): 0 / Redundancy: 3.1 % / Rmerge(I) obs: 0.122 / Rsym value: 0.122 / Net I/σ(I): 6.8 |
Reflection shell | Resolution: 2.95→3.06 Å / Rmerge(I) obs: 0.617 / Mean I/σ(I) obs: 1.8 / Rsym value: 0.617 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.95→30 Å / Cor.coef. Fo:Fc: 0.928 / Cor.coef. Fo:Fc free: 0.875 / SU B: 42.292 / SU ML: 0.358 / Cross valid method: THROUGHOUT / ESU R Free: 0.473 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.244 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.03 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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